5N9K

Crystal structure of human Protein kinase CK2 catalytic subunit in complex with the ATP-competitive, tight-binding dibenzofuran inhibitor TF107 (5)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PVR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6293Prior to the crystallization the inhibitor was solubilized in 100 % DMSO in a concentration of 10 mM. Then, this inhibitor stock solution was mixed in a Ratio of 1:10 with human CK2alpha (construct 1-335; solved with a Protein concentration of 8-10 mg/ml in 500 mM sodium chloride, 25 mM Tris/HCl pH 8.5). After a short time of incubation this mixture were mixed with reservoir solution [32 % (w/v) PEG4000, 0.2 M ammonium acetate, 0.1 M citrate pH 5.6] in a ratio of 2.5:1. 3.5 microliter of this final mixture was then equilibrated against the reservoir solution. The crystal growth was induced by seeding with 150 nanoliter seed suspension after an equilibration time of two days.
Crystal Properties
Matthews coefficientSolvent content
1.9637.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.876α = 90
b = 45.67β = 111.14
c = 63.753γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.99987SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6445.67990.0360.036173.337660
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.67870.6450.6450.7161.62.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2PVR1.64336.221.3537635182698.850.16480.16380.1843
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.834
f_angle_d0.68
f_chiral_restr0.049
f_bond_d0.004
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2779
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms57

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing